CMOP_Ce_IPG2
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ
ORGANISM(S): Caenorhabditis Elegans
SUBMITTER: Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmströ, Brunner E, Mohanty S, Lercher MJ, Hunziker PE, Aebersold R, von Mering C, Hengartner MO
PROVIDER: PAe000421 | PeptideAtlas |
REPOSITORIES: PeptideAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| PAe000421_811_search.params.tar.gz | Other | |||
| PAe000421_811_searchdatabase_sequest.fasta | Fasta | |||
| PAe000421_811_sequest.params | Other | |||
| PAe000421_RAW_201104160218.tar.gz | Other | |||
| PAe000421_README | Other |
Items per page: 5 1 - 5 of 11 |
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Project description:A computer program was used to create random amino acid sequences based on and restricted by physical shadow masks which will be used for lithography-based synthesis of peptides. The output from this algorithm was used to create peptides that were synthesized by Sigma Aldrich, and printed onto glass slides. The arrays contained 384 peptides printed in duplicate for each of 4 different mask designs. 52 different monoclonal antibodies were incubated on these microarrays and analyzed for their propensity to bind the peptides created from each mask set. The diversity of binding served as a proxy for the 'randomness' of these peptides, and provided information about how many masks are needed to truly generate random sequence peptides.
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Project description:This project used membrane-enriched proteomics to compare the membrane proteome of SW480 human colorectal cancer subclones that had been transfected with the full length coding sequence of the beta-6 integrin subunit under an overexpression promoter (SW480OE) against SW480 cells that had been transfected with an ‘empty’ mock vector (SW480M). Cell lysate samples were enriched for membrane proteins using a modified sodium carbonate stripping method before undergoing peptide immobilised pH gradient isoelectric focusing (IPG-IEF). Two IPG-IEF pH ranges were used to increase proteomic coverage: pH3-10 (broad range; BR) and pH3.5-4.5 (narrow range; NR). Each IPG-IEF strip was cut into 24 equal fractions and the peptides eluted. IPG-IEF of each pH range for both cell lines was performed in triplicate, resulting in four triplicate sets of 24 fractions. Data processing and bioinformatics: Spectra were identified against the *Homo sapiens* protein database (derived from Ensembl, Swiss-Prot and NCBI) using X!Tandem and the Global Proteome Machine (GPM) Tornado XE (build date 2010.12.01). GPM searches were set to tryptic peptides under GPM’s default fragment ion mass tolerance of 0.4Da and did not include semi-cleavage. Searches included single acid polymorphisms and default GPM residue modifications (oxidation,dioxidation, carbamidomethyl, deamidation, acetylation).
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